Re: [R] Proper / Improper scoring Rules

2009-08-13 Thread Donald Catanzaro, PhD
Hi All, I have done more background research (including Frank's book) so I feel that my second question is answered. However, as a novice R user I still have the following problem, accessing the output of predict. So simplifying my question, using the example provided in the Design package

Re: [R] what is the difference between the two logistic models?

2009-08-13 Thread Daniel Malter
As I wrote in my previous email, you need to pick up a methods book that deals with an introduction to regression analysis. Using factors in R means using dummy variable coding. The coefficients estimated in your model using factors indicate, the effect of teaching.method = 2 in comparison to

Re: [R] Proper / Improper scoring Rules

2009-08-13 Thread Daniel Malter
results=c(0.31,0.36,0.33) names(results)=c(y=good,y=better,y=best) results names(results)[results==max(results)] which(names(results)==(names(results)[results==max(results)])) More generally, however, avoid protected operators in your variable names (like the equality sign)! Rather choose

Re: [R] Slicing cra**y csv files

2009-08-13 Thread Patrick Connolly
On Wed, 12-Aug-2009 at 03:36AM -0700, jorgusch wrote: | | First of all, sorry for not giving all information. | | Secondly, thanks a lot. This is a real help!! I did not know, that you can | use names... | This is really simple and works great!!! | | If anyone is close enough to the people

Re: [R] Plotting sigma symbol with unicode and turning into pdf

2009-08-13 Thread Dieter Menne
Jonathan R. Blaufuss wrote: set.seed(1) Data=rnorm(100,sd=1) plot(density(Data)) text(25000,0.4, paste(\u03c3 = , format(round(sd(Data),digits=3),big.mark=,)), font=2, col=blue) That example gives a latin s in my Windows system. Using font=5 it

[R] Running an error-prone R script using 'source' command

2009-08-13 Thread Nir Shachaf
Hi All, I am running a semi-stable algorithms from an R script file using 'source'. At a certain point one of the algorithms will most probably return an error and crash the run. What I would like to do is to make [R] keep running and just skip to the next command line in the external script

[R] forcasting or predictive analysis

2009-08-13 Thread rajclinasia
Hi Every one, My question is I want to do forcasting or predictive analysis on some data and also genearte any graph based on the analysis. is it possible in R, if possible please give me the code it is very helpful for me. Thanks in Advance. -- View this message in context:

Re: [R] forcasting or predictive analysis

2009-08-13 Thread Stefan Grosse
On Thu, 13 Aug 2009 00:26:46 -0700 (PDT) rajclinasia r...@clinasia.com wrote: R My question is I want to do forcasting or predictive analysis on R some data and also genearte any graph based on the analysis. is it R possible in R, if possible please give me the code it is very R helpful for me.

[R] for(variable in [])do

2009-08-13 Thread Inchallah Yarab
In this code i try to calculate le difference between too number for two value of  th variable phase i have did this (output - read.csv2(C:/RM2Param.csv,sep=,))   OptimYear LRPhase   PriorLRPosition  OptimPosition 1  2009  -1  1.15641679414676  0.252662968666702 2  2009  -1 

Re: [R] paste first row string onto every string in column

2009-08-13 Thread Patrick Connolly
On Wed, 12-Aug-2009 at 09:06AM -0700, Jill Hollenbach wrote: | | Thanks so much everybody, this has been incredibly helpful--not only is my | immediate issue solved but I've learned a lot in the process. The lapply | solution is best for me, as I need flexibility to edit df's with varying |

Re: [R] for(variable in [])do

2009-08-13 Thread Allan Engelhardt
On 13/08/09 08:55, Inchallah Yarab wrote: [...] for (LRPhase in c(-1,1)) + {Phase1- output[output[,2]==LRPhase,]} Phase1- Phase1[order (Phase1[,6]),] [...] why when i write for LRPhase in c(1,-1), it gives me the result only for Phase = 1?? Because you re-assign the Phase1

Re: [R] Another Plotting Hint - changing fill color for points

2009-08-13 Thread Gavin Simpson
On Wed, 2009-08-12 at 23:36 -0400, Scott Sherrill-Mix wrote: I don't really use Word or .wmf but maybe try a high pixel count .png e.g. png('test.png',height=480*5,width=480*5,res=72*5) plot(1:10, col = red, bg = grey, pch=21, cex =1.7) dev.off() Scott An EPS is likely to give better

[R] resolved Re : for(variable in [])do

2009-08-13 Thread Inchallah Yarab
thank you very much Allan it works!! De : Allan Engelhardt all...@cybaea.com Cc : r-help@r-project.org Envoyé le : Jeudi, 13 Août 2009, 10h10mn 14s Objet : Re: [R] for(variable in [])do On 13/08/09 08:55, Inchallah Yarab wrote: [...] for (LRPhase  in

[R] un run run...

2009-08-13 Thread Nir Shachaf
Hi All, I am running an Rscript with a bunch of algorithms that are UNSTABLE under some parameter settings. At a certain point one of them sends error massage and my whole run STOPS! What I would like is to save the error massage in some file or variable and carry on to the next command line

Re: [R] un run run...

2009-08-13 Thread ONKELINX, Thierry
Here is an example in pseudo code. Instead of Object - function that can generate error Other things to do Do something like Object - try(function that can generate error) if(class(Object) == try-error){ things to do when an error occures } else { other things to do } HTH,

[R] Matrix addition function

2009-08-13 Thread Lina Rusyte
Hello,   What function can I use for matrices addition? I couldn’t find any information about it in the manual or in the internet. (A+B suits, when the number of matrixes is small, function sum() doesn’t suit for matrices addition, because it sums all variables in the matrices and produces

[R] Plotting shaded areas

2009-08-13 Thread Thomas Loridan
Hi I would like to plot the variation of some mean values with time, and have the standard deviation around the mean shaded on the plot. I could not find a way to have the shaded area on the curve with the default R commands, do I need a special package to do that? Or any idea of a way with the

[R] Problem - BRugs Package

2009-08-13 Thread Kurniawati Rahmi
Dear all, I have any problem for my R Program (R.2.8.0). I want to use Brugs Package, this package has been installed. But there are error messages : library(BRugs) Loading required package: coda Error: package 'coda' could not be loaded In addition: Warning messages: 1: package 'BRugs' was

[R] When using randomForest, what's the effect to set.seed?

2009-08-13 Thread Chang, C-Y.
Greetings, When reading the random forest manual by Liaw, in the examples set.seed is always used before building a forest. Does it matter if I don't set the seed? If I set a different seed manually each time I build a forest, will this give better randomness? Thank you all in advance! --

[R] using the RODBC for excel

2009-08-13 Thread Han Chin Chan
Hi,   I am trying to import data directly from an excel spreadsheet using the RODBC package. I am getting the following error messages, wondering if anyone can help me with it?   connection = odbcConnectExcel('D:\\R files\\TestData.xls') tables = sqlTables(connection) tables    TABLE_CAT

Re: [R] using cat()

2009-08-13 Thread tsgiss
Ricardo Rodríguez wrote: Please, could you give me an example about how to use cat() to read the value of a variable in a function? Any other way? I've found how to make it globally available, thus printing it, but I don't know how to read out the value of any variable within the

Re: [R] Slicing cra**y csv files

2009-08-13 Thread jorgusch
Patrick Connolly-4 wrote: Did you notice that the method creates a dataframe with no rows? Sure I did, but once data is in R in a proper format, you can create rows with R tools quite easily. Though, getting first step done, is not always obvious to me. Maybe this is a extrem case, but the

[R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread willow1980
Dear R users, I have a problem in plotting 3 dimensional graph using mixed models. My model is sur_prop ~ afr_c+I(afr_c^2)+I(afr_c^3)+byear_c+I(byear_c^2)+I(byear_c^3)+I(byear_c^4)+(1|Studyparish)+afr_c:byear_c

[R] [R-pkgs] TraMineR updated to version 1.4

2009-08-13 Thread Alexis Gabadinho
Dear R users, The TraMineR package for mining, describing and visualizing sequences of states or events, and more generally discrete sequential data has been updated to version 1.4. Many new functionalities have been added, among which: new metrics for computing distances between sequences,

[R] ncdf

2009-08-13 Thread Silke Troemel
Dear all, working with R under Linux, I am not able to install the ncdf-package. The following appears: install.packages(ncdf) Warnung in install.packages(ncdf) : argument 'lib' is missing: using '/user/silke/R/x86_64-unknown-linux-gnu-library/2.6' --- Please select a CRAN mirror for use in

Re: [R] Problem - BRugs Package

2009-08-13 Thread Dieter Menne
Kurniawati Rahmi wrote: I have any problem for my R Program (R.2.8.0). I want to use Brugs Package, this package has been installed. But there are error messages : library(BRugs) Loading required package: coda Error: package 'coda' could not be loaded 1: package 'BRugs' was

[R] helper lines in plot. From point to axis.

2009-08-13 Thread Andreas Christoffersen
This is a very basic question. I am just wondering if there is a function where i can choose a vector of points, and them helper lines are drawn. I am asking because lines seams to be a cumbersome way to do this. E.g. x - 1:36 plot(log(x,1.1),xlab=Number of months, ylab=Visits(1000),main=webpage

Re: [R] Map of UK Counties - to use in R

2009-08-13 Thread Roger Bivand
If your csv file has points, you can read into a data.frame using df - read.csv(file name) in the usual way (watch the decimal sign and use read.csv2() if need be), and coerce to a SpatialPointsDataFrame by saying coordinates(df) - c(long, lat) where long, lat are the names of the

Re: [R] Nominal variables in SVM?

2009-08-13 Thread Bernd Bischl
Noah Silverman wrote: Thanks for all the suggestions. My data was loaded in from a csv file with about 80 columns (3 of these columns are nominal) no specific settings for the nominal columns. Currently, if I call svm (e1071), I get an error about the nominal column. Do I need to tell R to

Re: [R] axis scale

2009-08-13 Thread Jim Lemon
maram salem wrote: Dear All, I'm trying to plot a histogram (with the relative frequencies as the Y axis), But the scale of the y axis is given by 0e+00, 1e-04, 2e-04, 3e-04,. Now, I have 2 questions 1- Does (1e-04=0.01831563)? 2- If this true,how can i change the given scale to

Re: [R] Plotting shaded areas

2009-08-13 Thread Jim Lemon
Thomas Loridan wrote: Hi I would like to plot the variation of some mean values with time, and have the standard deviation around the mean shaded on the plot. I could not find a way to have the shaded area on the curve with the default R commands, do I need a special package to do that? Or any

Re: [R] Proper / Improper scoring Rules

2009-08-13 Thread Frank E Harrell Jr
Donald Catanzaro, PhD wrote: Hi All, I have done more background research (including Frank's book) so I feel that my second question is answered. However, as a novice R user I still have the following problem, accessing the output of predict. So simplifying my question, using the example

Re: [R] axis scale

2009-08-13 Thread Andreas Christoffersen
2- If this true,how can i change the given scale to (0.01,0.03,0.05,0.07,0.09)? If you want to change the axis tickmarks you can buildt your plot with yaxt=n and then add an axis with what you want, e.g. axis(side=2,at=c(0.01,0.03,0.05,0.07,0.09),cex.axis=1,las=2) Hope this helps. If not

Re: [R] Running an error-prone R script using 'source' command

2009-08-13 Thread jim holtman
What do you mean without success? Can you provide specifics. They work fine for me. You need to give details of how you are using it in your script and what conditions you see that make you think it is not working. On Thu, Aug 13, 2009 at 3:21 AM, Nir Shachafnirshac...@gmail.com wrote: Hi

[R] Yet another plotting hint - choosing the proper device to produce plots for Word

2009-08-13 Thread Jason Rupert
Scott, Thanks for your response and insight. I call what I'm seeing - Not coloring within the lines :) When using pch 19, 20, or 21, it looks like the fill does no stay within the perimeter of the circle or properly fill the circle, i.e. some blank area left. It is demonstrated at the

Re: [R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread Duncan Murdoch
willow1980 wrote: Dear R users, I have a problem in plotting 3 dimensional graph using mixed models. My model is sur_prop ~ afr_c+I(afr_c^2)+I(afr_c^3)+byear_c+I(byear_c^2)+I(byear_c^3)+I(byear_c^4)+(1|Studyparish)+afr_c:byear_c

Re: [R] C-statistic comparison with partially paired datasets

2009-08-13 Thread Frank E Harrell Jr
Hanneke Wijnhoven wrote: Frank, Thank you for your quick response! I want to compare the discriminative capacity of different anthropometric measures in predicting mortality, focussing on the thin site of these measures. Since these associations are not linear (U shaped for BMI and inversily

[R] Longer Dash using lty

2009-08-13 Thread Jason Rupert
By any chance is there a way to make the lty dashes longer? Ideally it would work kind of like the following: plot(-4:4, -4:4, type = n) abline(-5,-4:4, lty=dashed) abline(-2,-4:4, lty=longdash) # long dash words (love this) abline(-4:4,-4:4, lty=longerdash) I read the lty documentation that

[R] need technique for speeding up R dataframe individual element insertion (no deletion though)

2009-08-13 Thread Ishwor
Hi fellas, I am working on a dataframe cam and it involves comparison within the 2 columns - t1 and t2 on about 20K rows and 14 columns. ### cap = cam; # this doesn't take long. ~1 secs. for( i in 1:length(cam$end_date)) { x1=strptime(cam$end_date[i], %d/%m/%Y);

Re: [R] need technique for speeding up R dataframe individual element insertion (no deletion though)

2009-08-13 Thread jim holtman
First of all, do the strptime conversions one time outside the loop. I would guess that if you ran Rprof on the code, most of the time is in that routine -- did you run Rprof? Also you are going through the loop one too many times; your ending value is 'length(cam$end_date)' and then you are

Re: [R] problem loading ncdf library on MAC

2009-08-13 Thread Dan Kelley
Update: I could not get RNetCDF working because I couldn't install udunits version 1 properly, and udunits2 is not the right version. However, returning to the original post, I *did* get ncdf working. Just install it from source. Then, you can do as e.g. below pre library(ncdf) jpeg(SSS.jpg,

Re: [R] Longer Dash using lty

2009-08-13 Thread jim holtman
?par Look at line type specification: Line Type Specification Line types can either be specified by giving an index into a small built-in table of line types (1 = solid, 2 = dashed, etc, see lty above) or directly as the lengths of on/off stretches of line. This is done with a string of an even

Re: [R] Yet another plotting hint - choosing the proper device to produce plots for Word

2009-08-13 Thread Gavin Simpson
On Thu, 2009-08-13 at 04:53 -0700, Jason Rupert wrote: Scott, Thanks for your response and insight. I call what I'm seeing - Not coloring within the lines :) When using pch 19, 20, or 21, it looks like the fill does no stay within the perimeter of the circle or properly fill the

Re: [R] need technique for speeding up R dataframe individual element insertion (no deletion though)

2009-08-13 Thread Bill.Venables
Why do you need an explicit loop at all? (Also, your loop goes over i in 1:length(cam$end_date) but your code refers to cam$end_date[i+1] --||--!!) Here is a suggestion. You want to identify places where the date increases but the volume does not change. OK, where? ind - with(cam, {

[R] Limited number of replicates in qcc()?

2009-08-13 Thread Katrien Baert
Dear R-users, I'm encoutering some problems with the qcc()-function. When there are more than 25 replicates per sample the estimate for the standard deviation becomes NA, implying that nothing is plotted (error message: Error in plot.window(...) : need finite 'ylim' values) On the forum I

[R] Output to screen and file at the same time

2009-08-13 Thread Michael Knudsen
Hello! Using the sink function, output from R may be written to a file instead of the screen. I would really like to write my output to a file while running an R script and at the same time view the output live on my screen. Is there are way to do that? Thanks, Michael -- Michael Knudsen

Re: [R] ncdf

2009-08-13 Thread Stefan Grosse
On Thu, 13 Aug 2009 11:29:40 +0200 Silke Troemel silke.troe...@uni-bonn.de wrote: ST /usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld: ST /usr/local/lib64/libnetcdf.a(attr.o): relocation R_X86_64_32S ST against `a local symbol' can not be used when making a shared ST

Re: [R] Output to screen and file at the same time

2009-08-13 Thread Gabor Grothendieck
See the split argument in ?sink On Thu, Aug 13, 2009 at 9:01 AM, Michael Knudsenmicknud...@gmail.com wrote: Hello! Using the sink function, output from R may be written to a file instead of the screen. I would really like to write my output to a file while running an R script and at the same

Re: [R] Matrix addition function

2009-08-13 Thread Michael Knudsen
On Thu, Aug 13, 2009 at 11:35 AM, Lina Rusyteliner...@yahoo.co.uk wrote: Hi Lina, What function can I use for matrices addition? I couldn’t find any information about it in the manual or in the internet. (A+B suits, when the number of matrixes is small, function sum() doesn’t suit for

[R] R code to reproduce (while studying) Bates Watts 1988

2009-08-13 Thread Ottorino-Luca Pantani
Hi R users, I'm here trying to understand correlated residuals in nonlinear estimation. I'm reading/studying the book Bates, D. M. and D. G. Watts, (1988), /Nonlinear regression analysis and its applications/, Wiley, NY. pages 92-94, trying to reproduce the figures and to find out the code in

Re: [R] C-statistic comparison with partially paired datasets

2009-08-13 Thread hwijnh
Frank, thank you very much for your answer. Yes, I also estimated splines like you suggested but wanted to add more custom analyses as well. Your answer does help me however, thanks. Hanneke Hanneke Wijnhoven wrote: Frank, Thank you for your quick response! I want to compare the

[R] R graphics

2009-08-13 Thread Mcdonald, Grant
Dear sir, I am trying to create a barplot for two propotions, with proportions successful on the y and age on the x. So my data is in the formate of one vector containing 0s and 1s (i.e.successful or not) with a corresponding two level vector of age. successage 1

[R] Between-group variance from ANOVA

2009-08-13 Thread emj83
I have done some ANOVA tables for some data that I have, from this I can read the within-group variance. can anyone tell me how i may find out the between-group variance? Thanks Emma -- View this message in context:

Re: [R] Matrix addition function

2009-08-13 Thread Gabor Grothendieck
If A, B and C are matrices then: L - list(A, B, C) Reduce(+, L) On Thu, Aug 13, 2009 at 5:35 AM, Lina Rusyteliner...@yahoo.co.uk wrote: Hello, What function can I use for matrices addition? I couldn’t find any information about it in the manual or in the internet. (A+B suits, when the

Re: [R] R graphics

2009-08-13 Thread Achim Zeileis
On Thu, 13 Aug 2009, Mcdonald, Grant wrote: Dear sir, I am trying to create a barplot for two propotions, with proportions successful on the y and age on the x. So my data is in the formate of one vector containing 0s and 1s (i.e.successful or not) with a corresponding two level vector

[R] Whittle estimation for ARMA models

2009-08-13 Thread tzygmund mcfarlane
Hi, Does anyone know of a package/script that will implement the Whittle (1953) estimator for the parameters of an invertible stationary ARMA time series model? The estimator is defined on, for example, pg. 378 of Brockwell Davis (1991). I assume that the internal call .whittle in this code due

[R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread mauede
Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to assign a mnemnic name

[R] metafor random effects meta-analysis

2009-08-13 Thread Mark Urban
Hello, Great to see the new metafor package for meta-analysis. I would like to perform a meta-analysis in which I initially calculate the intercept of the model with a nested random-effects structure. In lme, this would be model- lme(v3~1, random=~1|species/study, weights = varFixed(~Wt),

Re: [R] When using randomForest, what's the effect to set.seed?

2009-08-13 Thread Daniel Malter
if you set a seed manually, it makes the results reproducible. That is, if you set a specific seed, your randomForest procedure should produce the exact same result every time (all others equal). As an example: set.seed(1234) rnorm(100) rnorm(100) set.seed(4531) rnorm(100) rnorm(100)

Re: [R] xyplot and subscripts

2009-08-13 Thread Juliet Hannah
I'm not sure how to do this in lattice, but here is an option with ggplot2. library(ggplot2) set.seed(123) # Make sure the data has a variable that indicates # which group is red and which one is black DF - data.frame(x = rnorm(10), y = rnorm(10), gr = rep(1:5, 2),endpoint =

[R] Browser and Debug?

2009-08-13 Thread Inchallah Yarab
Hi, Someone can explain to me how use Browser and Debug ? thank you [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Validity check when setting slot

2009-08-13 Thread Vitalie S.
Hi, RG Hi, RG I'm wondering if the following behaviour is normal: RG setClass('A', representation(number='numeric'), RG validity=function(object){ RG if( obj...@number -1 ) return(Invalid number); TRUE}) [1] A RG a - new('A') RG a An object of class

Re: [R] Browser and Debug?

2009-08-13 Thread Erik Iverson
This article might help: http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-tools.pdf -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Inchallah Yarab Sent: Thursday, August 13, 2009 9:40 AM To: r-help@r-project.org Subject: [R]

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Philipp Pagel
On Thu, Aug 13, 2009 at 04:05:07PM +0200, mau...@alice.it wrote: Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be

Re: [R] prop.test() - need algorithm or reference

2009-08-13 Thread Ronggui Huang
The help page of prop.test gives you three references. Isn't it enough? For example, Newcombe R.G. (1998) Two-Sided Confidence Intervals for the Single Proportion: Comparison of Seven Methods. _Statistics in Medicine_ *17*, 857-872. Newcombe R.G. (1998) Interval Estimation

Re: [R] Matrix addition function

2009-08-13 Thread Vitalie S.
On Thu, 13 Aug 2009 15:11:03 +0200, Michael Knudsen micknud...@gmail.com wrote: On Thu, Aug 13, 2009 at 11:35 AM, Lina Rusyteliner...@yahoo.co.uk wrote: Hi Lina, What function can I use for matrices addition? I couldn’t find any information about it in the manual or in the internet.

[R] How to get the n (number of observations) per conditional group

2009-08-13 Thread Dax
Hello all, I have a huge data set that I'm cleaning up a bit. I am extracted the means per condition, but also need to get the n. Strangely enough I am unable to find a function that could actually pull this off. I am unable to use replications or count the rows using nrow. What I am trying to

[R] [R-pkgs] dcemri: A package for medical image analysis

2009-08-13 Thread Brandon . J . Whitcher
dcemri 0.10 has been released on CRAN dcemri is (to the best of my knowledge) the first public-domain software package for the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI or DWI). Data import and export is availble for ANALYZE or NIfTI

Re: [R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread willow1980
Dear Professor Murdoch, That is exactly the difficulty for me. I don't know how to make a prediction with lmer using expand.grid; at the moment, I can use “mo...@x%*%fixef(model)” to get predicted values for existing observational data, but not data by expand.grid. Actually, if I know this, I can

[R] FW: R graphics

2009-08-13 Thread Mcdonald, Grant
From: Mcdonald, Grant Sent: 13 August 2009 13:08 To: r-help@R-project.org Subject: R graphics Dear sir, I am trying to create a barplot showing propotions, So my data is in the format of a vector containing 0s and 1s (i.e.successful or not) with a

Re: [R] How to get the n (number of observations) per conditional group

2009-08-13 Thread Erik Iverson
We will only be able to help if you provide a reproducible example! I'm sure this is a simple one-liner, but it's hard to tell from your example what it should be. The functions table, length, tapply, and/or nrow may play a part though. -Original Message- From:

[R] how to extract the order of genes after clustering

2009-08-13 Thread Rnewbie
Dear all, I used hclust() to generate a dendrogram. After clustering, I wanted to take the order of the genes for further plotting purposes. Anyone has an idea how I can reoder my raw gene list as it is shown in the dendrogram? Thanks in advance. -- View this message in context:

Re: [R] Yet another plotting hint - choosing the proper device to produce plots for Word

2009-08-13 Thread Jason Rupert
Magically, the eps version seems to fix the not coloring in the lines issue observed when using the WMF device - note that the issue was observed when viewing it on the screen and after printing it out. However, with eps, the color of the points when using pch 21 appears to stay within the

Re: [R] Output to screen and file at the same time

2009-08-13 Thread Greg Snow
You may also want to look at ?TeachingDemos::txtStart as an alternative to sink, one advantage is that the commands as well as the output can be included. With a little more work you can also include graphical output into a transcript file. Hope this helps, -- Gregory (Greg) L. Snow Ph.D.

Re: [R] Browser and Debug?

2009-08-13 Thread roger koenker
At points of total desperation you can always consider the time-honored, avuncular advice -- RTFM, in this case Section 4.4 of Writing R Extensions. url:www.econ.uiuc.edu/~rogerRoger Koenker emailrkoen...@uiuc.eduDepartment of Economics vox: 217-333-4558

Re: [R] metafor random effects meta-analysis

2009-08-13 Thread Viechtbauer Wolfgang (STAT)
Correct, it is not possible to fix the residual variance to 1 in the R version of lme(), which is what one (typically) wants to do in meta-analyses, where the sampling variances are assumed to be (approximately) known. This is however possible in S-Plus, if you have access to that. Adding:

Re: [R] paste first row string onto every string in column

2009-08-13 Thread Gene Leynes
I'm also a newbie, but I've been getting loads of utility out of the grep function and it's cousin gsub. Using asterisks are tricky because * often means anything of any length in a search pattern (e.g. delete *.* means delete all your files!). To find the literal * using grep you would need to

[R] Solutions of equation systems

2009-08-13 Thread Moreno Mancosu
Hello all! Maybe it's a newbie question(in fact I _am_, a newbie), but I hope you'll find the solution. I have an equation system which has k equation and n variables (kn). I would like to obtain a description of the solutions (which can be the equation of lines or a plane, or everything

Re: [R] How to plot 3-D surface graph from lmer mixed models?

2009-08-13 Thread Deepayan Sarkar
On Thu, Aug 13, 2009 at 6:34 AM, willow1980jianghua@shef.ac.uk wrote: Dear Professor Murdoch, That is exactly the difficulty for me. I don't know how to make a prediction with lmer using expand.grid; at the moment, I can use “mo...@x%*%fixef(model)” to get predicted values for existing

[R] split number in a vector and then make a chron object out of it

2009-08-13 Thread stephen sefick
These are date and times in the format MMDDhhmmss. I would like to take this column and make a chron object form them. I have tried a couple of the split family of functions but they need character input here is the data: date.time - c(19851001001500, 19851001003000, 19851001004500,

[R] some help with plotting a beautiful structure using rgl

2009-08-13 Thread Nair, Murlidharan T
Hi!! I need some help in using the correct required symbol when plotting my DNA structure using rgl. I need to plot one strand using empty circles and the other using filled circles and if possible have sequence in the center. I tried using pch and lty but have not been able to get it to do

Re: [R] split number in a vector and then make a chron object out of it

2009-08-13 Thread Henrique Dallazuanna
Try this: strptime(date.time, %Y%m%d%H%M%s) On Thu, Aug 13, 2009 at 1:59 PM, stephen sefick ssef...@gmail.com wrote: These are date and times in the format MMDDhhmmss. I would like to take this column and make a chron object form them. I have tried a couple of the split family of

Re: [R] split number in a vector and then make a chron object out of it

2009-08-13 Thread John Kane
I'm not sure that I understand your problem but if you want the vector in character rather than numeric try: library(Hmisc) library(Hmisc) time.date- Cs(19851001001500, 19851001003000, 19851001004500, 1985100101, 19851001011500, 19851001013000, 19851001014500, 1985100102,

Re: [R] SOLVED: Lattice: How to do error bars

2009-08-13 Thread Deepayan Sarkar
On Wed, Aug 12, 2009 at 7:19 AM, am...@xs4all.nl wrote: Thank you Gerrit, Your suggestion proved right after all: This does put error bars (dy) on the points. You only need to figure out the proper y axis scaling. xyplot(y~x|f,data=xy,groups=dy,panel=function(x,y,groups,subscripts,...)

Re: [R] How to get the n (number of observations) per conditional group

2009-08-13 Thread John Kane
?length --- On Thu, 8/13/09, Dax rienk.doet...@gmail.com wrote: From: Dax rienk.doet...@gmail.com Subject: [R] How to get the n (number of observations) per conditional group To: r-help@r-project.org Received: Thursday, August 13, 2009, 10:11 AM Hello all, I have a huge data set that I'm

[R] Efficiently Extracting Meta Data from TM Corpora

2009-08-13 Thread Shad Thomas
I'm using text miner (the tm package) to process large numbers of blog and message board postings (about 245,000). Does anyone have any advice for how to efficiently extract the meta data from a corpus of this size? TM does a great job of using MPI for many functions (e.g. tmMap) which

Re: [R] xyplot and subscripts

2009-08-13 Thread Deepayan Sarkar
On Thu, Aug 6, 2009 at 7:27 AM, Kito Palaxoukitopala...@yahoo.com wrote: Hi all, I have a data frame like this: DF - data.frame(x = rnorm(10), y = rnorm(10), gr = rep(1:5, 2)) and I make the following xy-plot: library(lattice) xyplot(y ~ x, data = DF, groups = gr, type = b, col = 1)

Re: [R] split number in a vector and then make a chron object out of it

2009-08-13 Thread Gabor Grothendieck
Try this: as.chron(date.time, %Y%m%d%H%M%S) On Thu, Aug 13, 2009 at 12:59 PM, stephen sefickssef...@gmail.com wrote: These are date and times in the format MMDDhhmmss.  I would like to take this column and make a chron object form them.  I have tried a couple of the split family of

[R] Fitting a quasipoisson distribution to univariate data

2009-08-13 Thread Nigel Harding
Dear all, I am analyzing counts of seabirds made from line transects at sea. I have been fitting Poisson and negative binomial distributions to the data using the goodfit function from the vcd library. I would also like to evaluate how well a quasi-poisson distribution fits the data. However,

[R] multiple downloads of data when evaluating plot() vs. xyplot()

2009-08-13 Thread Greg Hirson
I have noticed an interesting behavior when comparing how the base plot() function deals with a data argument that downloads data from the internet vs. how xyplot() in lattice performs the same task. The goal is to plot hourly temperature data. The data is downloaded and formatted for R using

Re: [R] Fitting a quasipoisson distribution to univariate data

2009-08-13 Thread Achim Zeileis
On Thu, 13 Aug 2009, Nigel Harding wrote: Dear all, I am analyzing counts of seabirds made from line transects at sea. I have been fitting Poisson and negative binomial distributions to the data using the goodfit function from the vcd library. I would also like to evaluate how well a

Re: [R] some help with plotting a beautiful structure using rgl

2009-08-13 Thread Nair, Murlidharan T
Ok, I was able to figure out one part by using rgl.spheres. I am still trying to insert text using rgl.texts. Does any one have a simple example? -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Nair, Murlidharan T Sent:

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to

[R] shading between two smoothed curves

2009-08-13 Thread Graves, Gregory
I have a set of 52 weekly values, one is the desired high lake stage for a week, and the other is the desired low lake stage for each week. It looks like this: week High Low 1 16 14.5 2 16 14.5 3 15.95 14.45 4 15.84 14.34 5 15.73 14.23 6 15.61 14.11 7 15.5 14 8 15.38

[R] reading a string

2009-08-13 Thread Mohsen Jafarikia
Hello All: I am having the following data file named data.dat Number of people Number of pets Age of trees ifn - data.dat dat - read.table(ifn) colnames(dat)-c(Variables) I want R to read all these in a string but when I ask R to read these, it gives me error because there more than one

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to

Re: [R] reading a string

2009-08-13 Thread Henrique Dallazuanna
Use readLines indeed. On Thu, Aug 13, 2009 at 3:21 PM, Mohsen Jafarikia jafari...@gmail.comwrote: Hello All: I am having the following data file named data.dat Number of people Number of pets Age of trees ifn - data.dat dat - read.table(ifn) colnames(dat)-c(Variables) I want R to

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to

[R] Point-to-point Truncation with truncreg possible?

2009-08-13 Thread Vivek Ayer
Hi all, Can you use the truncreg() function to do point-to-point truncation, i.e., specify a different point=, for each point in your dataset. I guess in that sense this would be a nonlinear fit. Thanks, Vivek __ R-help@r-project.org mailing list

Re: [R] how to get R interpreter to remember constant values without using any memory location

2009-08-13 Thread Ben Bolker
mauede wrote: Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to

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